I couldn't stand the Section 31 genocide plot on DS9. The worst part of it was that parts of the Federation wanted it to succeed.
Is this Federation worth saving?
Would you be happy as a citizen to see the Federation government fall and be replaced by either the Dominion, Klingons, Romulans or the Cardassians?
While I think the Federation takes the whole "we are explorers" things a little too far and encroaches on other species territory (see Cestus III), the Dominion kicked in the door and deserved whatever ass-whuppin' the Federation could dish out. Including the destruction of the Founders.
Same thing goes for the Borg.